Dutch Society for Mass Spectrometry

Hey #TeamMassSpec,

Many non-human proteomics studies still search against taxon-filtered FASTAs.

❌ Redundant sequences
❌ Inflated search space
✅ Reference proteomes cut redundancy, improve annotation, and make results comparable.

👉 Time to move beyond taxon filters. #proteomics #massspec #uniprot

Breaking barriers in the sensitive and accurate mass determination of large DNA plasmids by mass photometry Heck and colleagues developed a mass photometry-based method for accurate and fast mass determination of plasmid DNA. Conventional mass photometry methods are not applicable for large DNA particles; h...

Breaking barriers in the sensitive and accurate mass determination of large DNA plasmids by mass photometry: Molecular Therapy Nucleic Acids www.cell.com/molecular-th.... Even visualizing > 10 million Da plasmids by the incredible Eduard Ebberink

Modanovo: A Unified Model for Post-Translational Modification-Aware de Novo Sequencing Using Experimental Spectra from In Vivo and Synthetic Peptides Post-translational modifications (PTMs) play a central role in cellular regulation and are implicated in numerous diseases. Database searching remains the standard for identifying modified peptides fr...

Excited to share Modanovo, our transformer-based method for de novo peptide sequencing, which supports a broad range of post-translational modifications (PTMs)!
www.biorxiv.org/content/10.1...
#proteomics #massspectrometry #PTM

Molecular Characterization of Natural Organic Matter Using Complementary Liquid Chromatography–Mass Spectrometry and Gas Chromatography–Mass Spectrometry Techniques Given the impact of natural organic matter (NOM) on water quality and treatment, understanding its properties is essential in water chemistry. However…

Molecular Characterization of Natural Organic Matter Using Complementary Liquid Chromatography–Mass Spectrometry and Gas Chromatography–Mass Spectrometry Techniques #JChromA www.sciencedirect.com/science/arti...

What does a language model know about proteins? www.nature.com/artic...

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#proteomics #prot-paper

Great news! 🎉 The abstract deadline is extended to Oct 7, 2025! Don’t miss your chance to share your work 🚀 #NVMS #MassSpec

Join us for the NVMS Fall Meeting 2025 with the Dutch Mass Spec community!!!🧪✨😀

📅 19 November 2025
📍 House of Connections, Groningen

🎤 Present your research! Submit an abstract for a poster or oral presentation: www.nvms.nl/index.php/re...

Your NVMS Board

#NVMS2025 #MassSpec

Slice-PASEF: Maximising Ion Utilisation in LC-MS Proteomics Quantitative mass spectrometry (MS)-based proteomics has become a streamlined technology with a wide range of usage. Many emerging applications, such as single-cell proteomics, spatial proteomics of t...

www.biorxiv.org/content/10.1...

🕷️Spiders in your blood? Don’t worry, these are protein molecules of C4BP protein, part of your immune system. Just like real spiders, they grab prey with their “legs.” Watch them in action! Intrigued, check the paper of @tkadava.bsky.social doi.org/10.1016/j.mc... @bijvoet-centre.bsky.social

Ångström-resolution imaging of cell-surface glycans - Nature Nanotechnology By combining bioorthogonal metabolic labelling and resolution enhancement through sequential imaging of DNA barcodes, the molecular organization of individual sugars in the native glycocalyx has been ...

New paper online:

Ångström-resolution imaging of cell-surface glycans.

The molecular organization of sugars in the native #glycocalyx has been resolved at 9 ångström using bioorthogonal metabolic labeling and #superresolution imaging of DNA barcodes.

#Glycotime

www.nature.com/articles/s41...

Enhancing Tandem MS Sensitivity and Peptide Identification via Ion Preaccumulation in an Orbitrap Mass Spectrometer High-throughput mass spectrometry-based proteomics has gained increasing interest for both academic and industrial applications. As implementation of faster gradients has facilitated higher sample thr...

Boosting Orbitrap MS/MS speed to ∼70 Hz? 🚀

Read how we did it in our latest paper 👇

pubs.acs.org/doi/10.1021/...

A transformer model for de novo sequencing of data-independent acquisition mass spectrometry data - Nature Methods Cascadia is a mass spectrometry-based de novo sequencing model that uses a transformer architecture to handle data-independent acquisition data and achieves substantially improved performance across a...

www.nature.com/articles/s41...

A transformer model for de novo sequencing of data-independent acquisition mass spectrometry data - Nature Methods Cascadia is a mass spectrometry-based de novo sequencing model that uses a transformer architecture to handle data-independent acquisition data and achieves substantially improved performance across a...

We’re excited to announce the publication of Cascadia, our new de novo sequencing model designed for DIA data. By extending the transformer architecture to fully capture the complexities of DIA data, we achieve state-of-the-art performance.

www.nature.com/articles/s41...

Are you looking forward to attending #EuPA2025 in beautiful Saint-Malo? Get ready for an enriching experience in extraordinary #proteomics!

🗓️ Mark your calendar for the SCIEX lunch symposium, taking place on Wednesday, June 18!

🔗 Full show agenda 👉 bit.ly/3HcA6Hw

#SkepticsWelcome #ZenoTOF8600

Free structural MS hands-on workshop @ BIOCEV (CZ)

📅 Sept 15–19, 2025

For PhDs, postdocs & undergrads (CZ/SK)

HDX-MS, native MS, cross-linking, high-res MS, data processing

Apply by July 31 → bit.ly/3HNyzIg

@spidocs.bsky.social @mbuavcr.bsky.social @ciisbinstructcz.bsky.social

🌞Wishing everyone in the mass spec community a fantastic summer break!

Whether you are kicking back with the NVMS summer newsletter 👉 www.nvms.nl/index.php/nv... or diving into fresh data, wishing you sunshine, fun, and great results! 😄

#MassSpec #NVMS

Increased EThcD efficiency on the hybrid Orbitrap Excedion Pro Mass Analyzer extends the depth in identification and sequence coverage of HLA class I immunopeptidomes Gaining a complete and unbiased understanding of the non-tryptic peptide repertoire presented by HLA-I complexes by LC-MS/MS is indispensable for therapy design for cancer, autoimmunity and infectious...

We explored the Excedion Pro Mass Analyzer with faster & more efficient EThcD capabilities, launched @asms.org, to more efficiently convert MS2 spectra to PSMs, as quality & unambiguous identification are more important parameters than peptide numbers. www.biorxiv.org/content/10.1...

Couldn’t find and forgot to tag @lperezpaneda.bsky.social on this, she did awesome work analyzing the data!

Engineering Life 2025: ORIGIN AND FUNCTION OF MECHANICAL FORCES IN BIOLOGY Engineering Life 2025, biological forces, force spectroscopy, measuring forces, developmental forces, molecular motors, forces in morphogenesis, cytoskeleton, DNA mechanics, bionanotechnology

📢Conference alert📢

Only one week left to register for the Engineering Life 2025 Symposium at Dresden September 1-3. This year's edition focuses on the function of mechanical forces in biology.

engineering-life-dresden.de

Assessment of false discovery rate control in tandem mass spectrometry analysis using entrapment www.nature.com/artic...

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#proteomics #prot-paper

🚨 Preprint alert 🚨 | Justin J.J. van der Hooft 🚨 Preprint alert 🚨 --> Large-scale unsupervised mass spectral discovery with improved annotation and customized searching by MS2LDA 2.0 Very proud of Laura Rosina Torres Ortega, Jonas Dietrich, a...

🚨 Preprint alert 🚨
--> Large-scale unsupervised mass spectral discovery with improved annotation and customized searching by MS2LDA 2.0

#metabolomics #CompMetabolomics #software #substructure #annotation #data #patterns #MolNetEnhancer #networking

www.linkedin.com/posts/jjjvan...

NVMS Spring Meeting 2025 - 1/3 📢
What a fantastic NVMS Spring Meeting at Sanquin Research in Amsterdam! The day was packed with cutting-edge mass spec talks, and a great atmosphere for networking. A big thank you to all speakers, attendees, and sponsors who made it such a success! 👍👏
www.nvms.nl

NVMS Spring Meeting 2025 - 2/3 📢
We were proud to see so many excellent talks from young researchers! Special congratulations to Alienke van Pijkeren (RUG) winner of the youngNVMS poster prize for her exciting work on single-cell proteomics. Great science and well-deserved recognition!👍👏
www.nvms.nl

NVMS Spring Meeting 2025 - 3/3 📢
At the General Assembly, we reviewed activities, and unanimously confirmed anoukrijs.bsky.social for a second term as NVMS Chair. Thank you, Anouk, for your continued dedication to the Dutch mass spec community!
📸 Don’t miss the full recap on our website: www.nvms.nl

🚨 NVMS Spring Meeting: Program Announced! 🚨
26th May 2025 | Sanquin, Amsterdam
The agenda is live – and the event is fully booked!
Still want to join? Check the program and add your name to the waiting list: www.nvms.nl/index.php/nv...

#NVMS #MassSpec

Excited to announce our revamped PhD-level BioMS course this September:

Advanced Proteomics for Drug Discovery and Biotherapeutics

Great line-up of instructors and topics, registration is open:
www.hecklab.com/advanced-pro...

Do-It-Yourself De Novo Antibody Sequencing Workflow that Achieves Complete Accuracy of the Variable Regions Antibodies are widely used as research tools or therapeutic agents. Knowing the sequences of the variable regions of an antibody─both the heavy chain and the light chain─is a prerequisite for the production of recombinant antibodies. Mass spectrometry-based de novo sequencing is a frequently used, and sometimes the only approach to gaining this information. Here, we describe a workflow that enables accurate sequence determination of monoclonal antibodies based on mass spectrometry data and freely available software tools. This workflow, which we developed using a homemade anti-FLAG monoclonal antibody as a reference sample, achieved 100% accuracy of the variable regions with clear distinction between leucine (L) and isoleucine (I). Using this workflow, we successfully decoded a monoclonal anti-HA antibody, for which we had no prior knowledge of its sequence. Based on the de novo sequencing result, we generated a recombinant anti-HA antibody, and demonstrated that it has the same specificity, sensitivity, and affinity as the commercial antibody.

Do-It-Yourself De Novo Antibody Sequencing Workflow that Achieves Complete Accuracy of the Variable Regions #JProteomeRes #MassSpec pubs.acs.org/doi/10.1021/...

In-depth plasma N-glycoproteome profiling using narrow-window data-independent acquisition on the Orbitrap Astral mass spectrometer Nature Communications - While DIA has advanced standard proteomics, its application in glycoproteomics has remained limited. Here, the authors present an optimized narrow-window DIA method for...

rdcu.be/ehinQ Read how a $1,- piece of cotton makes the difference for Shelley Jager enabling in-depth plasma N-glycoproteome profiling

📢Just 3 months to go until the 16th MaxQuant Summer School! #MQSS2025
Join us in Utrecht, Netherlands from July 21–25, 2025, for a week of in-depth training in mass-spectrometry-based proteomics.
Register now: eventbrite.de/e/maxquant-s...
#TeamMassSpec

The NVMS Spring Meeting at Sanquin, Amsterdam, on May 26th is almost here! 🌟

🔬 Abstract submission is still open for oral & poster presentations, send you abstract to: program@nvms.nl, deadline: April 7th

Registration link is on our website: www.nvms.nl

#NVMS #MassSpectrometry #Amsterdam #Sanquin